PONE-D-24-37521The Variable Selection of Two-part Regression Model for Semicontinuous DataPLOS ONE

Dear Dr. Yahui,

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3. Thank you for stating the following financial disclosure: [Research of A. Liu is supported by the

Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development. Lu’s work is supported by the research foundation of Zhejiang University of Science and Technology (2023QN094) and Hangzhou philosophy and social science planning project (Z23JC042).]. Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf.

Additional Editor Comments:

The two reviewers had very different feelings about the paper contribution. Reading the paper myself, I have to say that my impression is closer to that of reviewer 2, which recommends its rejection due to the absence of novel statistical methods and to limited simulation and empirical exercises.

Nevertheless, even though the methodological contribution is very minor at most, the paper is well written and deals with an interesting problem.

So, also considering reviewer 1 evaluation, my recommendation is for a major revision, in case the authors are motivated to do so. It should incorporate changes and additions according to all the points raised by the reviewers, especially reviewer 2. There are some deep points raised there, which should all be dealt with to build a newer version of the paper.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: No

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: No

Reviewer #2: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The data was not made available. Also, I suggest that the authors specify which software was used to conduct the analyses. Additionally, if feasible, making the code for the simulations and applications available to readers would enhance the paper’s transparency and reproducibility.

Reviewer #2: In this paper, authors proposed methods for variable selection for the two-part regression model specifically, the Bernoulli-Normal two-part (BNT) regression model. The variable selection method is based on adaptive Lasso penalty function. The following are detailed comments:

1. The usage of normal model for the non-zero part is limited. In reality, often the continuous measure does not follow normal distribution.

2. It would be interesting to see the model performance for the following scenarios

a) Varying Zero Proportions including low, moderate, and high zero proportions

b) Different Variable-Effect Strengths including strong and weak signal between predictors and outcome in one or both parts of the model.

c) Different Correlations Between Parts. The current simulation assumes independent parts. However, it will be useful to test the robustness of the model under the violation of the independence assumption.

d) It is not clear the model performance with high-dimensional data. The current simulation assumes the largest number of covariates in the model is 25.

e) Simulate scenarios where some predictors only influence the zero part, while others only influence the non-zero part. This will test the method’s capacity to select variables that are important for only one part of the model. The current simulation assumes the same covariates for both parts of the model.

f) Simulate cases where the model is misspecified for one or both parts, to test how robust the variable selection method is to model misspecification.

3. There is no software available publicly. It is hard for other researchers to implement the proposed approach.

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Reviewer #1: No

Reviewer #2: No

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Attachments

Attachment

Submitted filename: comments - PONE-D-24-37521.pdf

The Variable Selection of Two-part Regression Model for Semicontinuous Data

PONE-D-24-37521R1

Dear Dr. Yahui,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Flavio A. Ziegelmann, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments:

I agree with the two reviewers. The authors have satisfactorily dealt with all the issues raised by them in the first round. The only pending issue is the possible lack of data availability, which is still mentioned by one of the reviewers.

Comments to the Author

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: No

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

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